Hi Here is the suggestions I got from one of the docking developers.
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use pose docking instead of regular docking in rosetta++. This can be done simply by adding “-pose” to the command line. I ran this command line with “-pose” and without “-pose” and in normal docking, dock_pert 0 0 0 does indeed create some decoys that are significantly perturbed from the starting structure. I did not see this when using pose docking.
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> I am trying to perform a local protein docking. The two docking partners are 5 A away from the native complex. What would be te right command to dock these structures locally. I tried to set the -dock_pert flag to 0 0 0. This still resulted in large numbers of decoys that where rotated with more than 80 degrees and translated more than 10 A.
> This is the command I used:
> rosetta AA 0001 _ -dock -dock_mcm -dock_rtmin -dock_pert 0 0 0 -s 0001.pdb -nstruct 200
>
> Thanks,
.
